Craniofacial morphogenesis is a complex process requiring coordinated proliferation, movement and differentiation of six distinct facial prominences. The complexity of this process leaves it vulnerable to environmental and genetic perturbations, such that craniofacial malformations are one of the most common classes of birth defects. Facial prominences are made up of a mono-layer of ectoderm encasing a large core of neural crest- and mesodermally-derived mesenchymal cells. Signaling from this minor population of ectodermal cells directs and coordinates the behavior of the underlying mesenchyme, and thence facial morphogenesis. Manipulations that alter these signaling processes and tissue interactions have grave consequences for facial development, resulting in various types of medically important dysmorphology including orofacial clefting. Thus a detailed knowledge of geno-dynamics of the ectoderm is an essential component of the overall description of facial development. In this application a multi-disciplinary team has been assembled with expertise in craniofacial biology, mouse molecular genetics, bioinformatics and computer biology to gain a Systems Biology level understanding of early mammalian facial development. In Aim 1, the ectoderm and the mesenchyme of the wild-type facial prominences will be separated at critical timepoints encompassing facial morphogenesis, then these separated tissues will be used to generate contrasting dynamic spatio-temporal profiles of chromatin signatures, gene expression and translation. These studies will then be extended to abnormal development by perturbing crucial signaling pathways and regulatory mechanisms within the facial ectoderm. In this respect, new evidence from mouse models indicates that loss of tissue-specific epithelial splicing factors results in orofacial clefting. In Aim 2, these mice ill be used to interrogate the alternatively sliced transcripts that rely upon these Esrp proteins to direct normal facial development (Aim 2). How these changes alter transcript levels and transcript isoforms in the ectoderm, and how this subsequently impacts the underlying mesenchyme will be studies in detail. These studies should provide a valuable resource detailing the dynamic interplay of ectoderm and mesenchyme in both normal facial development and craniofacial deformity. Tissue-specific of deletion of genes within the ectoderm is a further way to perturb normal facial development. Mouse models are available based on the Hedgehog, Wnt and Fgf signaling pathways that development serious craniofacial defects upon deregulation in the ectoderm. These models will be studied in Aim 3 to investigate the critical epithelial:mesenchymal interactions underpinning facial development.